Crash if HPO term not found.

TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities

https://thejacksonlaboratory.github.io/LIRICAL/stable

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Crash if HPO term not found. #398

Closed pnrobinson closed 5 years ago

pnrobinson commented 5 years ago

In LiricalTemplate with the phenopacket Blanco-Kelly-2017-CDH3-Patient.json the HPO term id HP:0410400 is not being found. This id is from a term that was created just recently, "HP:0410400","Absent sebaceous glands". LIRICAL was running on an hp.obo file from the previous release. The solution is to update the hp.obo file, but we do not want the program to crash without a clear error warning. Implement this during the Phenopacket import.

pnrobinson commented 5 years ago

I have modified the code so that the user gets an interpretable error message if an "unknown" HPO term is used. LIRICAL crashes in this case under the assumption that users will not want to finish the analysis if there are problems with the input data. LIRICAL will also automatically replace any obsolete term ids with the current term id, and will output a warning to the command line.